ENST00000718234.1:n.319+11085C>T

Variant names:

• chr7-24308272-G-A
• rs16089
• ENST00000718234.1:n.319+11085C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000718234.1(ENSG00000228944):​n.319+11085C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000269 in 148,876 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.000027 (0 hom., cov: 28)
• Consequence: ENSG00000228944 ENST00000718234.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 2 publications found

Genes affected

ENSG00000228944 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986777	XR_001745121.2	n.209+11085C>T		intron_variant	Intron 2 of 2
LOC107986777	XR_001745122.2	n.81-111243C>T		intron_variant	Intron 1 of 1
LOC107986777	XR_001745123.2	n.209+11085C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228944	ENST00000718234.1	n.319+11085C>T		intron_variant	Intron 2 of 3
ENSG00000228944	ENST00000745512.1	n.341+11085C>T		intron_variant	Intron 2 of 5
ENSG00000228944	ENST00000745513.1	n.309+11085C>T		intron_variant	Intron 2 of 3
ENSG00000228944	ENST00000745514.1	n.328+11085C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0000269 AC: 4 AN: 148758 Hom.: 0 Cov.: 28

Gnomad AFR AF: 0.0000745

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000148

Gnomad OTH AF: 0.00

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0000269 AC: 4 AN: 148876 Hom.: 0 Cov.: 28 AF XY: 0.0000138 AC XY: 1 AN XY: 72384

African (AFR) AF: 0.0000743 AC: 3 AN: 40374

American (AMR) AF: 0.00 AC: 0 AN: 14500

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3452

East Asian (EAS) AF: 0.00 AC: 0 AN: 5022

South Asian (SAS) AF: 0.00 AC: 0 AN: 4768

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9902

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000148 AC: 1 AN: 67602

Other (OTH) AF: 0.00 AC: 0 AN: 2054

Alfa AF: 0.00 Hom.: 16988

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.88
PhyloP100		0.16

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs16089; hg19: chr7-24347891;